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- PDB-1zao: Crystal Structure of A.fulgidus Rio2 Kinase Complexed With ATP an... -

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Basic information

Entry
Database: PDB / ID: 1zao
TitleCrystal Structure of A.fulgidus Rio2 Kinase Complexed With ATP and Manganese Ions
ComponentsRio2 serine kinase
KeywordsTRANSFERASE / serine kinase / winged-helix / RIO domain / ATP-Mn complex / rRNA processing
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / protein serine/threonine/tyrosine kinase activity / ATP binding / metal ion binding
Similarity search - Function
RIO2 kinase winged helix domain, N-terminal / Rio2, N-terminal / RIO1 family / RIO-like kinase / RIO kinase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Tyrosine-protein kinase, active site / Winged helix DNA-binding domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily ...RIO2 kinase winged helix domain, N-terminal / Rio2, N-terminal / RIO1 family / RIO-like kinase / RIO kinase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Tyrosine-protein kinase, active site / Winged helix DNA-binding domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / PHOSPHATE ION / RIO-type serine/threonine-protein kinase Rio2
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsLaronde-Leblanc, N. / Guszczynski, T. / Copeland, T. / Wlodawer, A.
CitationJournal: Febs J. / Year: 2005
Title: Autophosphorylation of Archaeoglobus fulgidus Rio2 and crystal structures of its nucleotide-metal ion complexes.
Authors: Laronde-Leblanc, N. / Guszczynski, T. / Copeland, T. / Wlodawer, A.
History
DepositionApr 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rio2 serine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6326
Polymers32,8581
Non-polymers7745
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.862, 44.365, 62.793
Angle α, β, γ (deg.)90.00, 94.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Rio2 serine kinase


Mass: 32857.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: Rio2 / Plasmid: pDEST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-pLysS-DE3 / References: UniProt: O30245

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Non-polymers , 5 types, 333 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.78
Details: PEG 900, SODIUM PHOSPHATE, SODIUM CITRATE , pH 3.78, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99997 / Wavelength: 0.99997 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 8, 2004
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 1.84→63.25 Å / Num. all: 28175 / Num. obs: 27131 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.035
Reflection shellResolution: 1.84→1.887 Å / Redundancy: 3.8 % / Rsym value: 0.114 / % possible all: 68.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TQI
Resolution: 1.84→63.25 Å / Cor.coef. Fo:Fc: 0.952 / SU B: 1.938 / SU ML: 0.062 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 1361 5 %RANDOM
Rwork0.1835 ---
obs0.1835 27131 96.25 %-
all-26765 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.191 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20.84 Å2
2---0.47 Å20 Å2
3---1.06 Å2
Refine analyzeLuzzati coordinate error obs: 0.186 Å
Refinement stepCycle: LAST / Resolution: 1.84→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 42 328 2574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222285
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9713085
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7135268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58723.684114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07115409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9551518
X-RAY DIFFRACTIONr_chiral_restr0.0970.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021702
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21099
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21554
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1591.51390
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75322156
X-RAY DIFFRACTIONr_scbond_it2.89231036
X-RAY DIFFRACTIONr_scangle_it4.534.5929
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.839→1.887 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 61 -
Rwork0.197 1401 -
obs--68.31 %

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